{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0235TTEW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0235TTEW",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW274"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5643OMJV](/auxiliary-sets/IGVFDS5643OMJV/) has sequence file(s) [IGVFFI9278ZHKN](/sequence-files/IGVFFI9278ZHKN/), [IGVFFI7489SMJE](/sequence-files/IGVFFI7489SMJE/), [IGVFFI3014EZLH](/sequence-files/IGVFFI3014EZLH/), [IGVFFI2461RALG](/sequence-files/IGVFFI2461RALG/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5643OMJV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5643OMJV](/auxiliary-sets/IGVFDS5643OMJV/) has sequence file(s): [IGVFFI9278ZHKN](/sequence-files/IGVFFI9278ZHKN/), [IGVFFI7489SMJE](/sequence-files/IGVFFI7489SMJE/), [IGVFFI3014EZLH](/sequence-files/IGVFFI3014EZLH/), [IGVFFI2461RALG](/sequence-files/IGVFFI2461RALG/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS5643OMJV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0235TTEW](/measurement-sets/IGVFDS0235TTEW/) has sequence file(s) [IGVFFI6038BMYJ](/sequence-files/IGVFFI6038BMYJ/), [IGVFFI4652AGGF](/sequence-files/IGVFFI4652AGGF/), [IGVFFI8407VPIG](/sequence-files/IGVFFI8407VPIG/), [IGVFFI3624OKUE](/sequence-files/IGVFFI3624OKUE/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS0235TTEW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0235TTEW](/measurement-sets/IGVFDS0235TTEW/) has sequence file(s): [IGVFFI6038BMYJ](/sequence-files/IGVFFI6038BMYJ/), [IGVFFI4652AGGF](/sequence-files/IGVFFI4652AGGF/), [IGVFFI8407VPIG](/sequence-files/IGVFFI8407VPIG/), [IGVFFI3624OKUE](/sequence-files/IGVFFI3624OKUE/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS0235TTEW/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5514EBWS](/auxiliary-sets/IGVFDS5514EBWS/) has sequence file(s) [IGVFFI8633CSSL](/sequence-files/IGVFFI8633CSSL/), [IGVFFI4088GWUY](/sequence-files/IGVFFI4088GWUY/), [IGVFFI3088BUJP](/sequence-files/IGVFFI3088BUJP/), [IGVFFI5368RJHA](/sequence-files/IGVFFI5368RJHA/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5514EBWS/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5514EBWS](/auxiliary-sets/IGVFDS5514EBWS/) has sequence file(s): [IGVFFI8633CSSL](/sequence-files/IGVFFI8633CSSL/), [IGVFFI4088GWUY](/sequence-files/IGVFFI4088GWUY/), [IGVFFI3088BUJP](/sequence-files/IGVFFI3088BUJP/), [IGVFFI5368RJHA](/sequence-files/IGVFFI5368RJHA/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS5514EBWS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5514EBWS/",
"accession": "IGVFDS5514EBWS",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_PB_LW274"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5643OMJV/",
"accession": "IGVFDS5643OMJV",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_PB_LW274"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
}
],
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/95d84f03-8ce0-489c-a755-f33ced139c5d/",
"title": "Gary Hon"
},
"title": "Multiscale functional characterization of genomic variation in human developmental disorders"
},
"control_for": [],
"creation_timestamp": "2024-04-25T21:58:47.235340+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6038BMYJ/",
"accession": "IGVFFI6038BMYJ",
"aliases": [
"gary-hon:LW274_8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:39:39.328590+00:00",
"file_format": "fastq",
"file_size": 11802185223,
"href": "/sequence-files/IGVFFI6038BMYJ/@@download/IGVFFI6038BMYJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/2b203abc-379d-4e50-b884-2f2b3b7c84bf/IGVFFI6038BMYJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW274_S6_L008_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4652AGGF/",
"accession": "IGVFFI4652AGGF",
"aliases": [
"gary-hon:LW274_8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:39:27.079396+00:00",
"file_format": "fastq",
"file_size": 967392610,
"href": "/sequence-files/IGVFFI4652AGGF/@@download/IGVFFI4652AGGF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/24282a0d-2e8c-4440-9f4e-af7f72600ae9/IGVFFI4652AGGF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW274_S6_L008_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8407VPIG/",
"accession": "IGVFFI8407VPIG",
"aliases": [
"gary-hon:LW274_8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:39:14.357524+00:00",
"file_format": "fastq",
"file_size": 1007826176,
"href": "/sequence-files/IGVFFI8407VPIG/@@download/IGVFFI8407VPIG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/96ed301e-32c5-4460-ac19-288a4f3ae7b4/IGVFFI8407VPIG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW274_S6_L008_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3624OKUE/",
"accession": "IGVFFI3624OKUE",
"aliases": [
"gary-hon:LW274_8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:41:23.727937+00:00",
"file_format": "fastq",
"file_size": 11860209074,
"href": "/sequence-files/IGVFFI3624OKUE/@@download/IGVFFI3624OKUE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/eb9839e7-b863-40fc-b0b6-cf7ba56a2ef5/IGVFFI3624OKUE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW274_S6_L008_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4762GRIW/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"preferred_assay_title": "Perturb-seq",
"protocols": [
"https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5849QIEI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5849QIEI",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW274"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9629YZLO/",
"accession": "IGVFDS9629YZLO",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW274), female, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-04-25T22:39:14.357524+00:00",
"submitter_comment": "Transcriptiome for LW274",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "0b4d36d5-8fb8-4562-85b2-68f7a6715f2e"
}